Pauley started 2006 in Portland. He posted a 2–3 with a 2.39 ERA in 10 starts for the Sea Dogs before making his major league debut on May 31 starting for Boston in place of the injured David Wells. He pitched 4⅓ innings against the Toronto Blue Jays and did not record a decision. In his 16 innings pitched for the Boston Red Sox, Pauley recorded a 7.88 ERA.

The Angels signed Pauley to a minor league contract on March 23, 2012. He was called up to the majors on May 7, 2012, but was designated for assignment on May 24. He cleared waivers and was then recalled to the Angels on June 12, 2012. He was designated for assignment a second time on June 18, and was claimed by the Toronto Blue Jays on June 20.[5]

Pauley was claimed by the Blue Jays on June 20 after being designated for assignment by the Angels for a second time. For the Blue Jays, Pauley sported a 0-1 record with a 6.48 ERA in 10 relief appearances. He was designated for assignment after he gave up 3 earned runs, on 3 hits vs. the Kansas City Royals on July 2. On July 9, he elected free agency.

The Seattle Mariners signed him to a minor league contract on July 12, and assigned him to the Triple-A Tacoma Rainiers on July 14. On August 24, 2012, it was announced Pauley had violated drug agreement while in Triple-A. He will be suspended 50 games.[6]

On June 10, 2013, Pauley signed a minor-league deal with the Arizona Diamondbacks and was assigned to Triple-A Reno.[7] After pitching in 4 games for the Aces, Pauley was released. In those 4 games, he went 0-1, giving up 10 hits and 7 runs in 5.2 innings.

Pauley is a sinkerball pitcher,[8] and as such his success relies on his ability to keep the ball down in the strike zone, and when contact is made, to get ground-ball outs. Pauley also has the standard fastball, curveball, and changeup in his repertoire.[citation needed] His fastball hits the high 80 MPH range and his curveball has more of a sweeping motion than the standard 12-to-6 movement seen from most minor-league pitchers.[citation needed]